Commit fc0b1bdb authored by Aflitos, Saulo Alves's avatar Aflitos, Saulo Alves
Browse files

Fixed bwa index output, and dependency of matepair mapping on indexing

parent b4bbf71a
......@@ -96,7 +96,7 @@ def addCommand(cmd, data):
#DATABASE
bwtFile = "%s.bwt" % PREFIX
bwtRes = addCommand("bwa index -a is -p %(TARGET)s %(SOURCE)s", {"TARGET": bwtFile, "SOURCE": ASSEMBLY})
bwtRes = addCommand("bwa index -a is -p %(TARGET)s %(SOURCE)s", {"TARGET": PREFIX, "SOURCE": ASSEMBLY})
#SETUP
......@@ -145,7 +145,8 @@ for fileType in data:
print " ", fileType , "BWA IN ",[str(x) for x in res ]
mpMap = addCommand("bwa aln -t 80 %(PREFIX)s %(SOURCE)s > %(TARGET)s", {"TARGET": mapName, "SOURCE": res, "PREFIX": PREFIX})
print " ", fileType , "BWA OUT",[str(x) for x in mpMap]
data[fileType][fileName][0] = res
Depends( mpMap, bwtRes )
data[fileType][fileName][0] = res
data[fileType][fileName][1] = mpMap
......
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